Usually a trashed game happens because you've badly screwed a file somewhere, most often dialog(f).tlk or chitin.key. The next move is to bang your head hard against the screen as you consider a total reinstallation for the nth time and wonder just what you've lost in this crash. If you stop and think about it, it's the game files that get broken and not the installation information.
The obvious move is to install BGII, copy it across to another directory and use bgmain.exe to launch it, rather than baldur.exe, but this doesn't work with some additional mods installed (Shadows Over Soubar, for one).
So install a clean, un-modded copy of SoA or ToB and then burn it to DVD. Add all the mods you want to be sure that your mod will work with and then burn that installation to DVD as well. In case of trash, if you know which file you've just destroyed, then copy back just that file. If you don't know just where it's all gone pear-shaped, delete the entire HDD installation (DON'T uninstall it, just clear out the game directory) and copy back the required DVD. It's a lot faster and stress-free than re-installation. Lastly, copy/install back in your known-working modfiles and start debugging.
Backups: too much is said about backups and not enough is done. Once a month I burn my entire modding setup to DVD. Once a week I burn all changed data to CD. If my PC decides to eat its HDD, at the very most I'll lose a few hours' work. Think about it - CDs are UK£0.10 each in bulk and even DVDs are only UK£1.05 in bulk. Cheap enough and getting cheaper.
For those of you that have on-board RAID, know what it is and can afford/use it, put in a pair of small drives (40Gb-ish) and set them to RAID 0. At the end of each mod session, copy across the changed data - it takes seconds. You now have identical data sets on three different HDDs plus DVD and CD backups.
Data-loss-paranoia? Yep - you bet I suffer from it!!!!!!!

-Y-